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Hotfix: pin nf-validation #346

Merged
merged 7 commits into from
Mar 20, 2024
Merged

Hotfix: pin nf-validation #346

merged 7 commits into from
Mar 20, 2024

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jfy133
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@jfy133 jfy133 commented Mar 13, 2024

As requested here: #342

PR checklist

  • This comment contains a description of changes (with reason).
  • If you've fixed a bug or added code that should be tested, add tests!
  • If you've added a new tool - have you followed the pipeline conventions in the contribution docs
  • If necessary, also make a PR on the nf-core/funcscan branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • Usage Documentation in docs/usage.md is updated.
  • Output Documentation in docs/output.md is updated.
  • CHANGELOG.md is updated.
  • README.md is updated (including new tool citations and authors/contributors).

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jfy133 commented Mar 13, 2024

@nf-core-bot fix linting

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github-actions bot commented Mar 13, 2024 •
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nf-core lint overall result: Failed ❌

Posted for pipeline commit e80f5f2

+| ✅ 201 tests passed       |+
!| ❗   2 tests had warnings |!
-| ❌  17 tests failed       |-

❌ Test failures:

  • files_exist - File must be removed: lib/Utils.groovy
  • files_exist - File must be removed: lib/WorkflowMain.groovy
  • files_exist - File must be removed: lib/NfcoreTemplate.groovy
  • files_exist - File must be removed: lib/WorkflowFuncscan.groovy
  • files_exist - File must be removed: lib/nfcore_external_java_deps.jar
  • nextflow_config - Config default value incorrect: params.amp_ampcombi_cutoff is set as 0.4 in nextflow_schema.json but is 0 in nextflow.config.
  • files_unchanged - .github/CONTRIBUTING.md does not match the template
  • files_unchanged - .github/PULL_REQUEST_TEMPLATE.md does not match the template
  • files_unchanged - .github/workflows/branch.yml does not match the template
  • files_unchanged - .github/workflows/linting_comment.yml does not match the template
  • files_unchanged - .github/workflows/linting.yml does not match the template
  • files_unchanged - assets/email_template.html does not match the template
  • files_unchanged - assets/email_template.txt does not match the template
  • files_unchanged - assets/nf-core-funcscan_logo_light.png does not match the template
  • files_unchanged - docs/images/nf-core-funcscan_logo_light.png does not match the template
  • files_unchanged - docs/images/nf-core-funcscan_logo_dark.png does not match the template
  • files_unchanged - pyproject.toml does not match the template

❗ Test warnings:

  • nextflow_config - Config manifest.version should end in dev: 1.1.5
  • pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline

✅ Tests passed:

Run details

  • nf-core/tools version 2.13.1
  • Run at 2024-03-20 13:35:37

@jfy133 jfy133 requested review from jasmezz and Darcy220606 March 13, 2024 14:37
jasmezz
jasmezz approved these changes Mar 13, 2024
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Just need a decision for bakta version (see Slack), otherwise LGTM!

jfy133
jfy133 commented Mar 20, 2024
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Last thing, but I can't approve my own PR 😆

CHANGELOG.md Outdated Show resolved Hide resolved
@jasmezz jasmezz merged commit ec1f1b6 into master Mar 20, 2024
20 of 21 checks passed
@jasmezz jasmezz deleted the patch branch March 20, 2024 22:36
@jasmezz jasmezz mentioned this pull request Apr 4, 2024
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@Darcy220606 Darcy220606 Darcy220606 approved these changes

@jasmezz jasmezz jasmezz approved these changes

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@jfy133 @jasmezz @Darcy220606 @nf-core-bot